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Protein-coding cis-natural antisense transcripts have high and broad expression in Arabidopsis
1Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada N1G 2W1.
Plant Physiology
|March 5, 2013
Summary
Protein-coding cis-natural sense antisense transcripts (cis-NATs) in Arabidopsis are highly abundant and coexpressed. Their genomic locations are linked to a permissive chromatin environment, suggesting a role beyond small RNA production.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Eukaryotic genomes feature genes oriented to produce cis-natural sense antisense transcripts (cis-NATs).
- This gene orientation is linked to splice variant generation and natural antisense small RNA biogenesis.
Purpose of the Study:
- To investigate the characteristics of protein-coding cis-NATs in Arabidopsis thaliana.
- To explore the relationship between cis-NATs, chromatin structure, and small RNA production.
Main Methods:
- Analysis of existing genomic and transcriptomic data for Arabidopsis.
- Examination of chromatin features (nucleosome density, histone modifications) in cis-NAT-encoding genes.
- Small RNA sequencing from wild-type and mutant plants.
Main Results:
- Protein-coding cis-NATs in Arabidopsis exhibit high abundance, coexpression, and broad expression patterns.
- cis-NAT-encoding genes are associated with permissive chromatin: low nucleosome density, high H3K9ac, and low H3K27me3.
- Natural antisense small RNA production from cis-NATs appears limited, with similar small RNA mapping in mutants and wild-type plants.
Conclusions:
- The proximity and expression of protein-coding cis-NATs in Arabidopsis are influenced by a permissive chromatin environment.
- cis-NATs may have regulatory roles beyond small RNA biogenesis.
- Further research is needed to understand the prevalence and function of cis-NATs in other eukaryotes.
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